[buster-discuss] Anisotropic ADP only for selected atoms

[ClAuS Flensburg]

Dear Giacomo,

There is a mechanism to select specific atoms for anisotropic ADPs.
The default set is "nonHydrogen" - see the list of automatically
determined sets in $BDG_home/tnt/data/sets.dat and how BUSTER is
interpreting them for your specific model in LIST.html (Search for
"set definitions"). If you want to make all CD atoms have ADP's try

cat > ADP-CD.gelly <<EOF
NOTE BUSTER_ANISO_SET { ATOMTYPE CD }
EOF

See also [1] about sets.

Then run BUSTER with

    refine -M ADP -Gelly ADP-CD.gelly ...

Does this work for you?


If your data contains a good anomalous signal and the input file
contains them BUSTER will write F_ano/PHI_ano columns that are
automatically consumed by COOT to display anomalous maps.

Hope this helps.


With best wishes,

ClAuS & Gerard (for BUSTER Developers)
[1] https://www.globalphasing.com/buster/manual/gelly/manual/gelly2.html


On Thu, Oct 26, 2023 at 09:51:31PM +0100, Gerard Bricogne wrote:
> Dear Giacomo,
> 
>      Thank you for your enquiry. 
> 
>      At the moment we do not have such a selection mechanism, but let me
> suggest another approach. If your data were collected with a typical
> wavelength of about 1.0 Angstroem, Cadmium has an f" slightly above 2
> electrons, so you should be able to see them in an anomlous difference
> Fourier map. You could then use SHARP, with phases from your model given as
> external phase information, to refine ADPs for these "heavy atoms. Finally,
> you could then add these ADPS to the same Cd atoms in the PDB file of your
> model.
> 
>      Just a thought, with possibly a number of devils hiding in the details
> but with perhaps a chance of success.
> 
>      What is the resolution of your data? Where do you do your data
> collection?
> 
> 
>      With best wishes,
> 
>           Gerard.
> 
> --
> On Thu, Oct 26, 2023 at 05:28:39PM +0000, Giacomo  CARLONI wrote:
> > Dear Buster users,
> > 
> > I was wondering if there is a way to specify a subset of atoms to be refined with anisotropic ADP, while keeping the rest isotropic (1 TLS per chain).
> > 
> > I have a dataset at 2.0 A resolution with more than 30 Cadmium ions coming from the crystallization condition. The majority of them is not at full occupancy and often the best I can do is placing random waters nearby.  I would like to test if I can improve the situation by treating the metal ions anisotropically.
> > 
> > Thanks for your help,
> > 
> > Giacomo
> 
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